Orthology transfer maps only the conserved core of the Varroa destructor proteome and over-calls host absence two times in three

The ectoparasitic mite Varroa destructor is the principal threat to managed honey bees, and a test case for the genome-scale methods applied to non-model organisms, nearly all of which infer from orthology. We reconstructed the first genome-wide protein-interaction network for V. destructor (7,080 proteins, 335,914 interactions), whose modular structure exceeds a degree-preserving null by 368 standard deviations, but whose every edge is interolog-transferred and every node conserved at least to Eukaryota. None of the 791 genes lacking an orthologous group enters it — arithmetic rather than discovery — yet the excluded compartment is large and coherent. It comprises 3,161 genes (30.9% of the proteome), shorter and less annotated than the rest; an annotation-free genome search detects orphans in a tick genome at 4.0% against 70.4% for networked genes. Within the orthology-bearing compartment visibility is non-monotonic: the Acari-level bin (74.1%) falls below the Arthropoda-level bin (89.9%). The same logic applied to host comparison yields a benchmarked error: of genes called absent from Apis on group identity alone, 67.4% recover a sequence homologue — against zero for a shuffled null and 1.3% in the presence direction — rising to 78.3% in the least panel-biased stratum. Both figures are properties of the calling rule: under an identity floor the error directions cross near 34% identity; orthology cannot be said to err in either direction without fixing the criterion first. Host divergence resolves into gene absence and residue-level substitution, falling in those two compartments respectively. A bee-sparing target map follows as broader impact.